Add vignette on generating lockfile from log

[parmsam-pfizer]

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The spirit of logrx

While many packages to facilitate the logging of code already exist in the R ecosystem, it is hard to find a solution that works well for clinical programming applications. Many logging implementations are more implicit and rely on user input to create the log for the execution of a script. While this is useful for logging specific events of an application, in clinical programming a log has a set purpose.

logrx is built around the concept of creating a log for the execution of an R script that provides an overview of what happened as well as the environment that it happened in. We set out to create a flexible logging utility that could provide the necessary information to anyone reviewing the code execution so they can recreate the execution environment and run the code for themselves. Please make sure your Pull Request meets this spirit of logrx.

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• Code is formatted according to the tidyverse style guide
• Updated relevant unit tests or have written new unit tests. Remember to remove any configured log objects at the end of every test using log_remove().
• Creation/updates to relevant roxygen headers and examples.
• Run devtools::document() so all .Rd files in the man folder and the NAMESPACE file in the project root are updated appropriately
• Run pkgdown::build_site() and check that all affected examples are displayed correctly and that all new functions occur on the "Reference" page.
• Update NEWS.md if the changes pertain to a user-facing function (i.e. it has an @export tag) or documentation aimed at users (rather than developers)
• Address any updates needed for vignettes and/or templates
• Run R CMD check locally and address all errors and warnings - devtools::check()
• Link the issue so that it closes after successful merging. - fixes Feature Request: Consider adding ability to generate a renv lockfile from log #161
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[parmsam-pfizer]

Not sure if I need to add renv into the suggests section of the DESCRIPTION file. It's used in the vignette. Any thoughts @bms63 @nicholas-masel @thomasp-b @kodesiba?

Run options(crayon.enabled = TRUE)
── R CMD build ─────────────────────────────────────────────────────────────────
pdflatex not found! Not building PDF manual.
* checking for file ‘.../DESCRIPTION’ ... OK
* preparing ‘logrx’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Error: --- re-building ‘approved.Rmd’ using rmarkdown
--- finished re-building ‘approved.Rmd’
--- re-building ‘execution.Rmd’ using rmarkdown
--- finished re-building ‘execution.Rmd’
--- re-building ‘generate-lockfile.Rmd’ using rmarkdown
Quitting from lines [20](https://github.com/pharmaverse/logrx/actions/runs/13313538018/job/37181842469?pr=233#step:9:21)-24 [setup] (generate-lockfile.Rmd)
Error: Error: processing vignette 'generate-lockfile.Rmd' failed with diagnostics:
there is no package called 'renv'
--- failed re-building ‘generate-lockfile.Rmd’
--- re-building ‘logrx.Rmd’ using rmarkdown
--- finished re-building ‘logrx.Rmd’
--- re-building ‘options.Rmd’ using rmarkdown
--- finished re-building ‘options.Rmd’
SUMMARY: processing the following file failed:
  ‘generate-lockfile.Rmd’
Error: Error: Vignette re-building failed.
Execution halted
Error: Error in proc$get_built_file() : Build process failed
Calls: <Anonymous> ... build_package -> with_envvar -> force -> <Anonymous>
Execution halted
Error: Process completed with exit code 1.

[parmsam-pfizer]

Resolved based on short discussion on this in today's meeting.

[parmsam-pfizer]

Spell check failing due to "renv" and "lockfile" words which are used properly. That check for this PR can be ignored or maybe we can add those terms into the whitelist.

Run insightsengineering/r-spellcheck-action@v3
Run options(repos = c(CRAN = "https://cloud.r-project.org/"))
Loading required package: spelling
Run cd .
DESCRIPTION does not contain 'Language' field. Defaulting to 'en-US'.
  WORD       FOUND IN
lockfile   generate-lockfile.Rmd:2,52
renv       generate-lockfile.Rmd:2,52

Number of misspelled words: 2
You may correct the spellings of the words above or add them to the "inst/WORDLIST" file by running spelling::update_wordlist()
Error: Process completed with exit code 2.

[bms63]

So interesting these are passing now @kodesiba

[parmsam-pfizer]

Made a bunch of fixes last night, @bms63.

[kodesiba]

@parmsam-pfizer might be excessive but will this just record packages with the latest version or also the versions used? wasn't sure if that was even doable with this method or if we'd have to go all the way to an install and then lockfile create approach to capture that information.